R packages
gene regulatory networks
network topology

An R/Bioconductor package to analyze motifs in gene regulatory networks


Fabrício Almeida-Silva


December 27, 2022


The goal of magrene is to identify and analyze graph motifs containing duplicated genes in gene regulatory networks (GRNs). Possible motifs include V, PPI V, lambda, delta, and bifans.

Motif frequencies can be analyzed in the context of gene duplications to explore the impact of small-scale and whole-genome duplications on gene regulatory networks.

Additionally, GRNs can be tested for motif enrichment by comparing motif frequencies to a null distribution generated from degree-preserving simulated GRNs.

Finally, users can calculate the interaction similarity between gene pairs based on the Sorensen-Dice similarity index.